When I'm not running/connected to JoinFS, all by Superbug/Tacpack weapons work super.

When I run/connect to JoinFS, and I shoot a missile (for example... happens with HARM too) it comes off the rail, goes out about 100 ft, then levitates to 150,000 ft. Check out the screenshot. The exhaust goes vertical. And the inset view is of the missile sitting up there at 150,000 ft, but it drops down to 100,000 ft then pops back up to 150,000 ft, and will cycle like that.

The only thing that might cause that is if you have enabled ignore on that particular object. If you open at the aircraft list and tick the box in the bottom right of the window, 'List Ignored Aircraft'. Then fire the missile and click the Refresh button on the aircraft list, it should show the missile objects. If you select it you'll be able to see if you have ignored in the options at the bottom part of the window.